This study was conducted to develop and field-test a low cost protocol to estimate the isolate- and sample-level prevalence of resistance to critically important antibiotic drugs among
Escherichia coliand Salmonellaisolated from dairy cattle feces. E. coliand Salmonellawere isolated from and screened on selective media, with and without antibiotics respectively. Bacterial isolates were further tested for susceptibility to a suite of antibiotics using disk diffusion. Molecular methods were performed on select bacterial isolates to identify and distinguish genetic determinants associated with the observed phenotypes. Among 85 non-type-specific E. colirandomly isolated from MacConkey agar without antibiotics, the isolate-level prevalence of resistance to tetracycline was the highest (8.2%), there was no isolate resistant to third-generation cephalosporin (0.0%) and one isolate was resistant to nalidixic acid (1.2%). Among 37 E. colirecovered from MacConkey agar with cefotaxime at 1.0g/ml, 100% were resistant to ampicillin and 56.8% were resistant to a third-generation cephalosporin (ceftriaxone). Among 22 E. coliisolates recovered from MacConkey agar with ciprofloxacin at 0.5g/ml, 90.9% were resistant to tetracycline whereas 77.3% and 54.5% were resistant to nalidixic acid and ciprofloxacin respectively. Sixteen Salmonellawere isolated and only one demonstrated any resistance (i.e., single resistance to streptomycin). Among E. coliisolates that were either resistant or intermediate to ceftriaxone, an AmpC phenotype was more common than an extended spectrum beta-lactamase (ESBL) phenotype (29 versus 10 isolates, respectively). Among 24 E. coliisolates that were whole genome sequenced, phenotypic profiles of antibiotic resistance detected were generally substantiated by genotypic profiles. For instance, all isolates with an AmpC phenotype carried a blaCMY2 gene. The protocol used in this study is suited to detecting and estimating prevalence of antimicrobial resistance in bacteria isolated from food animal feces in resource-limited laboratories in the developing world.